Selecting specific slice from the summary table

classic Classic list List threaded Threaded
2 messages Options
Reply | Threaded
Open this post in threaded view
|

Selecting specific slice from the summary table

aw29
Hi!

I'm currently working on code that will allow me to threshold and analyze
two channels (1 and 2) for multiple images. The first channel works
perfectly, but the second one is having trouble transferring data to my
excel spreadsheet because of the "Process Stack?" pop-up window. After I go
through and do all of the thresholding and analysis, I get to this part:

IJ.run("Analyze Particles...", "summarize slice", );
IJ.renameResults("Results");
IJ.run("Read and Write Excel", "file_mode=queue_write sheet=Mouse_"+
filename);

However, I just realized that the pop-up window that comes up"Process
Stack?" after I run "Analyze Particles" is processing all three images and
not just the one that I am currently thresholding. Is there a way to select
"no" on the "Process Stack?" window when it asks me if I want to process all
three images?
Or could I possibly select "slice 2" from the summary table to send to the
excel spreadsheet if there isn't a way to select "no"?



                       
                       





--
Sent from: http://imagej.1557.x6.nabble.com/

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html
Reply | Threaded
Open this post in threaded view
|

Re: Selecting specific slice from the summary table

Cammer, Michael-2
When thresholding and filtering composite hyperstacks, I spilt channels first and then reassemble after the processing.
Cheers-
Michael

-----Original Message-----
From: aw29 <[hidden email]>
Sent: Thursday, April 11, 2019 10:04 AM
To: [hidden email]
Subject: Selecting specific slice from the summary table

Hi!

I'm currently working on code that will allow me to threshold and analyze two channels (1 and 2) for multiple images. The first channel works perfectly, but the second one is having trouble transferring data to my excel spreadsheet because of the "Process Stack?" pop-up window. After I go through and do all of the thresholding and analysis, I get to this part:

IJ.run("Analyze Particles...", "summarize slice", ); IJ.renameResults("Results"); IJ.run("Read and Write Excel", "file_mode=queue_write sheet=Mouse_"+ filename);

However, I just realized that the pop-up window that comes up"Process Stack?" after I run "Analyze Particles" is processing all three images and not just the one that I am currently thresholding. Is there a way to select "no" on the "Process Stack?" window when it asks me if I want to process all three images?
Or could I possibly select "slice 2" from the summary table to send to the excel spreadsheet if there isn't a way to select "no"?



                       
                       





--
Sent from: https://urldefense.proofpoint.com/v2/url?u=http-3A__imagej.1557.x6.nabble.com_&d=DwICAg&c=j5oPpO0eBH1iio48DtsedeElZfc04rx3ExJHeIIZuCs&r=E0xNnPAQpUbDiPlC50tp7rW2nBkvV7fujQf0RknE5bU&m=qP9a-RMxOQu411kpRmMX_86XZsiFvpvR3zCNYcLjI40&s=D5AblN_YAG9G8h8Ucm8wl7Qq2XfLV8AQG3-fF-MNow0&e=

--
ImageJ mailing list: https://urldefense.proofpoint.com/v2/url?u=http-3A__imagej.nih.gov_ij_list.html&d=DwICAg&c=j5oPpO0eBH1iio48DtsedeElZfc04rx3ExJHeIIZuCs&r=E0xNnPAQpUbDiPlC50tp7rW2nBkvV7fujQf0RknE5bU&m=qP9a-RMxOQu411kpRmMX_86XZsiFvpvR3zCNYcLjI40&s=8899SgLPyzGymX8ppuXpe6WjrcfLmV-8voe6W81Cc-k&e=

------------------------------------------------------------
This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain information that is proprietary, confidential, and exempt from disclosure under applicable law. Any unauthorized review, use, disclosure, or distribution is prohibited. If you have received this email in error please notify the sender by return email and delete the original message. Please note, the recipient should check this email and any attachments for the presence of viruses. The organization accepts no liability for any damage caused by any virus transmitted by this email.
=================================

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html